# Bio.Emboss.Applications module

Code to interact with and run various EMBOSS programs (OBSOLETE).

These classes follow the AbstractCommandline interfaces for running programs.

We have decided to remove this module in future, and instead recommend building your command and invoking it via the subprocess module directly.

class Bio.Emboss.Applications.Primer3Commandline(cmd='eprimer3', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the Primer3 interface from EMBOSS.

  The precise set of supported arguments depends on your version of EMBOSS. This version accepts arguments current at EMBOSS 6.1.0:

      >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
      >>> cline.explainflag = True
      >>> cline.osizeopt=20
      >>> cline.psizeopt=200
      >>> cline.outfile = "myresults.out"
      >>> cline.bogusparameter = 1967  # Invalid parameter
      Traceback (most recent call last):
          ...
      ValueError: Option name bogusparameter was not found.
      >>> print(cline)
      eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True

  __init__(cmd='eprimer3', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 124
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property dnaconc

    Nanomolar concentration of annealing oligos in the PCR.

    This controls the addition of the -dnaconc parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property excludedregion

    Regions to exclude from primer picking.

    This controls the addition of the -excludedregion parameter and its associated value. Set this property to the argument value required.

  property explainflag

    Produce output tags with eprimer3 statistics

    This controls the addition of the -explainflag parameter and its associated value. Set this property to the argument value required.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property forwardinput

    Sequence of a forward primer to check.

    This controls the addition of the -forwardinput parameter and its associated value. Set this property to the argument value required.

  property gcclamp

    The required number of Gs and Cs at the 3’ of each primer.

    This controls the addition of the -gcclamp parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property hybridprobe

    Find an internal oligo to use as a hyb probe.

    This controls the addition of the -hybridprobe parameter and its associated value. Set this property to the argument value required.

  property includedregion

    Subregion of the sequence in which to pick primers.

    This controls the addition of the -includedregion parameter and its associated value. Set this property to the argument value required.

  property maxdifftm

    Maximum difference in melting temperatures between forward and reverse primers.

    This controls the addition of the -maxdifftm parameter and its associated value. Set this property to the argument value required.

  property maxgc

    Maximum GC% for a primer.

    This controls the addition of the -maxgc parameter and its associated value. Set this property to the argument value required.

  property maxmispriming

    Maximum allowed similarity of primers to sequences in library specified by -mispriminglibrary

    This controls the addition of the -maxmispriming parameter and its associated value. Set this property to the argument value required.

  property maxpolyx

    Maximum allowable mononucleotide repeat length in a primer.

    This controls the addition of the -maxpolyx parameter and its associated value. Set this property to the argument value required.

  property maxsize

    Maximum length of a primer oligo.

    This controls the addition of the -maxsize parameter and its associated value. Set this property to the argument value required.

  property maxtm

    Maximum melting temperature for a primer oligo.

    This controls the addition of the -maxtm parameter and its associated value. Set this property to the argument value required.

  property mingc

    Minimum GC% for a primer.

    This controls the addition of the -mingc parameter and its associated value. Set this property to the argument value required.

  property minsize

    Minimum length of a primer oligo.

    This controls the addition of the -minsize parameter and its associated value. Set this property to the argument value required.

  property mintm

    Minimum melting temperature for a primer oligo.

    This controls the addition of the -mintm parameter and its associated value. Set this property to the argument value required.

  property mishyblibraryfile

    Library file of seqs to avoid internal oligo hybridisation.

    This controls the addition of the -mishyblibraryfile parameter and its associated value. Set this property to the argument value required.

  property mispriminglibraryfile

    File containing library of sequences to avoid amplifying

    This controls the addition of the -mispriminglibraryfile parameter and its associated value. Set this property to the argument value required.

  property numreturn

    Maximum number of primer pairs to return.

    This controls the addition of the -numreturn parameter and its associated value. Set this property to the argument value required.

  property oanyself

    Maximum allowable alignment score for self-complementarity.

    This controls the addition of the -oanyself parameter and its associated value. Set this property to the argument value required.

  property odnaconc

    Nanomolar concentration of internal oligo in the hybridisation.

    This controls the addition of the -odnaconc parameter and its associated value. Set this property to the argument value required.

  property oendself

    Max 3’-anchored self-complementarity global alignment score.

    This controls the addition of the -oendself parameter and its associated value. Set this property to the argument value required.

  property oexcludedregion

    Do not pick internal oligos in this region.

    This controls the addition of the -oexcludedregion parameter and its associated value. Set this property to the argument value required.

  property ogcmax

    Maximum GC% for internal oligo.

    This controls the addition of the -ogcmax parameter and its associated value. Set this property to the argument value required.

  property ogcmin

    Minimum GC% for internal oligo.

    This controls the addition of the -ogcmin parameter and its associated value. Set this property to the argument value required.

  property ogcopt

    Optimum GC% for internal oligo.

    This controls the addition of the -ogcopt parameter and its associated value. Set this property to the argument value required.

  property ogcpercent

    Optimum GC% for a primer.

    This controls the addition of the -ogcpercent parameter and its associated value. Set this property to the argument value required.

  property oligoinput

    Sequence of the internal oligo.

    This controls the addition of the -oligoinput parameter and its associated value. Set this property to the argument value required.

  property omaxsize

    Maximum length of internal oligo.

    This controls the addition of the -omaxsize parameter and its associated value. Set this property to the argument value required.

  property ominsize

    Minimum length of internal oligo.

    This controls the addition of the -ominsize parameter and its associated value. Set this property to the argument value required.

  property omishybmax

    Maximum alignment score for hybridisation of internal oligo to library specified by -mishyblibraryfile.

    This controls the addition of the -omishybmax parameter and its associated value. Set this property to the argument value required.

  property opolyxmax

    Maximum length of mononucleotide repeat in internal oligo.

    This controls the addition of the -opolyxmax parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property opttm

    Optimum melting temperature for a primer oligo.

    Option added in EMBOSS 6.6.0, replacing -otm

    This controls the addition of the -opttm parameter and its associated value. Set this property to the argument value required.

  property osaltconc

    Millimolar concentration of salt in the hybridisation.

    This controls the addition of the -osaltconc parameter and its associated value. Set this property to the argument value required.

  property osize

    Optimum length of a primer oligo.

    This controls the addition of the -osize parameter and its associated value. Set this property to the argument value required.

  property osizeopt

    Optimum length of internal oligo.

    This controls the addition of the -osizeopt parameter and its associated value. Set this property to the argument value required.

  property otm

    Melting temperature for primer oligo (OBSOLETE).

    Option replaced in EMBOSS 6.6.0 by -opttm

    This controls the addition of the -otm parameter and its associated value. Set this property to the argument value required.

  property otmmax

    Maximum melting temperature of internal oligo.

    This controls the addition of the -otmmax parameter and its associated value. Set this property to the argument value required.

  property otmmin

    Minimum melting temperature of internal oligo.

    This controls the addition of the -otmmin parameter and its associated value. Set this property to the argument value required.

  property otmopt

    Optimum melting temperature of internal oligo.

    This controls the addition of the -otmopt parameter and its associated value. Set this property to the argument value required.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property prange

    Acceptable range of length for the PCR product.

    This controls the addition of the -prange parameter and its associated value. Set this property to the argument value required.

  property psizeopt

    Optimum size for the PCR product.

    This controls the addition of the -psizeopt parameter and its associated value. Set this property to the argument value required.

  property ptmmax

    Maximum allowed melting temperature for the amplicon.

    This controls the addition of the -ptmmax parameter and its associated value. Set this property to the argument value required.

  property ptmmin

    Minimum allowed melting temperature for the amplicon.

    This controls the addition of the -ptmmin parameter and its associated value. Set this property to the argument value required.

  property ptmopt

    Optimum melting temperature for the PCR product.

    This controls the addition of the -ptmopt parameter and its associated value. Set this property to the argument value required.

  property reverseinput

    Sequence of a reverse primer to check.

    This controls the addition of the -reverseinput parameter and its associated value. Set this property to the argument value required.

  property saltconc

    Millimolar salt concentration in the PCR.

    This controls the addition of the -saltconc parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence to choose primers from.

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property target

    Sequence to target for flanking primers.

    This controls the addition of the -target parameter and its associated value. Set this property to the argument value required.

  property task

    Tell eprimer3 what task to perform.

    This controls the addition of the -task parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.PrimerSearchCommandline(cmd='primersearch', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the primersearch program from EMBOSS.

  __init__(cmd='primersearch', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 309
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property infile

    File containing the primer pairs to search for.

    This controls the addition of the -infile parameter and its associated value. Set this property to the argument value required.

  property mismatchpercent

    Allowed percentage mismatch (any integer value, default 0).

    This controls the addition of the -mismatchpercent parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property seqall

    Sequence to look for the primer pairs in.

    This controls the addition of the -seqall parameter and its associated value. Set this property to the argument value required.

  property snucleotide

    Sequences are nucleotide (boolean)

    This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

  property sprotein

    Sequences are protein (boolean)

    This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FDNADistCommandline(cmd='fdnadist', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fdnadist program from EMBOSS.

  fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for calculating distance matrices from DNA sequence files.

  __init__(cmd='fdnadist', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 345
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property basefreq

    specify basefreqs

    This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.

  property categories

    File of substitution rate categories

    This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property freqsfrom

    use empirical base freqs

    This controls the addition of the -freqsfrom parameter and its associated value. Set this property to the argument value required.

  property gamma

    This controls the addition of the -gamma parameter and its associated value. Set this property to the argument value required.

  property gammacoefficient

    value for gamma (> 0.001)

    This controls the addition of the -gammacoefficient parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property invarfrac

    proportoin of invariant sites

    This controls the addition of the -invarfrac parameter and its associated value. Set this property to the argument value required.

  property lower

    lower triangle matrix (y/N)

    This controls the addition of the -lower parameter and its associated value. Set this property to the argument value required.

  property method

    sub. model [f,k,j,l,s]

    This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

  property ncategories

    number of rate categories (1-9)

    This controls the addition of the -ncategories parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property rate

    rate for each category

    This controls the addition of the -rate parameter and its associated value. Set this property to the argument value required.

  property sequence

    seq file to use (phylip)

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property ttratio

    ts/tv ratio

    This controls the addition of the -ttratio parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property weights

    weights file

    This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FTreeDistCommandline(cmd='ftreedist', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the ftreedist program from EMBOSS.

  ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for calculating distance measures between phylogentic trees.

  __init__(cmd='ftreedist', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 381
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property dtype

    distance type ([S]ymetric, [b]ranch score)

    This controls the addition of the -dtype parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property intreefile

    tree file to score (phylip)

    This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

  property noroot

    treat trees as rooted [N/y]

    This controls the addition of the -noroot parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outgrno

    which taxon to root the trees with (starts from 0)

    This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

  property pairing

    tree pairing method ([A]djacent pairs, all [p]ossible pairs)

    This controls the addition of the -pairing parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property style

    output style - [V]erbose, [f]ill, [s]parse

    This controls the addition of the -style parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FNeighborCommandline(cmd='fneighbor', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fneighbor program from EMBOSS.

  fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for calculating neighbor-joining or UPGMA trees from distance matrices.

  __init__(cmd='fneighbor', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 412
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property datafile

    dist file to use (phylip)

    This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property jumble

    randommise input order (Y/n)

    This controls the addition of the -jumble parameter and its associated value. Set this property to the argument value required.

  property matrixtype

    is matrix square (S), upper (U) or lower (L)

    This controls the addition of the -matrixtype parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outgrno

    taxon to use as OG

    This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

  property outtreefile

    filename for output tree

    This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

  property progress

    print progress (Y/n)

    This controls the addition of the -progress parameter and its associated value. Set this property to the argument value required.

  property seed

    provide a random seed

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property treeprint

    print tree (Y/n)

    This controls the addition of the -treeprint parameter and its associated value. Set this property to the argument value required.

  property treetype

    nj or UPGMA tree (n/u)

    This controls the addition of the -treetype parameter and its associated value. Set this property to the argument value required.

  property trout

    write tree (Y/n)

    This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FSeqBootCommandline(cmd='fseqboot', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fseqboot program from EMBOSS.

  fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to pseudo-sample alignment files.

  __init__(cmd='fseqboot', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 444
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property blocksize

    print progress (Y/n)

    This controls the addition of the -blocksize parameter and its associated value. Set this property to the argument value required.

  property catergories

    file of input categories

    This controls the addition of the -categories parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property dotdiff

    Use dot-differencing? [Y/n]

    This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property fracsample

    fraction to resample

    This controls the addition of the -fracsample parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property jusweights

    what to write out [D]atasets of just [w]eights

    This controls the addition of the -justweights parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property regular

    absolute number to resample

    This controls the addition of the -regular parameter and its associated value. Set this property to the argument value required.

  property reps

    how many replicates, defaults to 100)

    This controls the addition of the -reps parameter and its associated value. Set this property to the argument value required.

  property rewriteformat

    output format ([P]hyilp, [n]exus, [x]ml

    This controls the addition of the -rewriteformat parameter and its associated value. Set this property to the argument value required.

  property seed

    specify random seed

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property seqtype

    output format ([D]na, [p]rotein, [r]na

    This controls the addition of the -seqtype parameter and its associated value. Set this property to the argument value required.

  property sequence

    seq file to sample (phylip)

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property test

    specify operation, default is bootstrap

    This controls the addition of the -test parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property weights

    weights file

    This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FDNAParsCommandline(cmd='fdnapars', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fdnapars program from EMBOSS.

  fdnapars is an EMBOSS version of the PHYLIP program dnapars, for estimating trees from DNA sequences using parsiomny. Calling this command without providing a value for the option “-intreefile” will invoke “interactive mode” (and as a result fail if called with subprocess) if “-auto” is not set to true.

  __init__(cmd='fdnapars', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 482
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property dotdiff

    Use dot-differencing? [Y/n]

    This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property intreefile

    Phylip tree file

    This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

  property maxtrees

    max trees to save during run

    This controls the addition of the -maxtrees parameter and its associated value. Set this property to the argument value required.

  property njumble

    number of times to randomise input order (default is 0)

    This controls the addition of the -njumble parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outgrno

    Specify outgroup

    This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

  property outtreefile

    filename for output tree

    This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

  property rearrange

    Rearrange on just 1 best tree (Y/n)

    This controls the addition of the -rearrange parameter and its associated value. Set this property to the argument value required.

  property seed

    provide random seed

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property sequence

    seq file to use (phylip)

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property thorough

    more thorough search (Y/n)

    This controls the addition of the -thorough parameter and its associated value. Set this property to the argument value required.

  property thresh

    Use threshold parsimony (y/N)

    This controls the addition of the -thresh parameter and its associated value. Set this property to the argument value required.

  property threshold

    Threshold value

    This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

  property transversion

    Use tranversion parsimony (y/N)

    This controls the addition of the -transversion parameter and its associated value. Set this property to the argument value required.

  property trout

    Write trees to file (Y/n)

    This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property weights

    weights file

    This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FProtParsCommandline(cmd='fprotpars', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fdnapars program from EMBOSS.

  fprotpars is an EMBOSS version of the PHYLIP program protpars, for estimating trees from protein sequences using parsiomny. Calling this command without providing a value for the option “-intreefile” will invoke “interactive mode” (and as a result fail if called with subprocess) if “-auto” is not set to true.

  __init__(cmd='fprotpars', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 524
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property dotdiff

    Use dot-differencing? [Y/n]

    This controls the addition of the -dotdiff parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property intreefile

    Phylip tree file to score

    This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

  property njumble

    number of times to randomise input order (default is 0)

    This controls the addition of the -njumble parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outgrno

    Specify outgroup

    This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

  property outtreefile

    phylip tree output file

    This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

  property seed

    provide random seed

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property sequence

    seq file to use (phylip)

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property thresh

    Use threshold parsimony (y/N)

    This controls the addition of the -thresh parameter and its associated value. Set this property to the argument value required.

  property threshold

    Threshold value

    This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

  property trout

    Write trees to file (Y/n)

    This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property weights

    weights file

    This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

  property whichcode

    which genetic code, [U,M,V,F,Y]]

    This controls the addition of the -whichcode parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FProtDistCommandline(cmd='fprotdist', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fprotdist program from EMBOSS.

  fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to estimate trees from protein sequences using parsimony

  __init__(cmd='fprotdist', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 566
  __static_attributes__ = ('parameters',)
  property aacateg

    Choose the category to use [G,C,H]

    This controls the addition of the -aacateg parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property basefreq

    DNA base frequencies (space separated list)

    This controls the addition of the -basefreq parameter and its associated value. Set this property to the argument value required.

  property catergories

    file of rates

    This controls the addition of the -catergories parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property ease

    Pob change category (float between -0 and 1)

    This controls the addition of the -ease parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gamma

    This controls the addition of the -gamma parameter and its associated value. Set this property to the argument value required.

  property gammacoefficient

    value for gamma (> 0.001)

    This controls the addition of the -gammacoefficient parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property invarcoefficient

    float for variation of substitution rate among sites

    This controls the addition of the -invarcoefficient parameter and its associated value. Set this property to the argument value required.

  property method

    sub. model [j,h,d,k,s,c]

    This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

  property ncategories

    number of rate categories (1-9)

    This controls the addition of the -ncategories parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property rate

    rate for each category

    This controls the addition of the -rate parameter and its associated value. Set this property to the argument value required.

  property sequence

    seq file to use (phylip)

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property ttratio

    Transition/transversion ratio (0-1)

    This controls the addition of the -ttratio parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property weights

    weights file

    This controls the addition of the -weights parameter and its associated value. Set this property to the argument value required.

  property whichcode

    genetic code [c,m,v,f,y]

    This controls the addition of the -whichcode parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.FConsenseCommandline(cmd='fconsense', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fconsense program from EMBOSS.

  fconsense is an EMBOSS wrapper for the PHYLIP program consense used to calculate consensus trees.

  __init__(cmd='fconsense', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 606
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property intreefile

    file with phylip trees to make consensus from

    This controls the addition of the -intreefile parameter and its associated value. Set this property to the argument value required.

  property method

    consensus method [s, mr, MRE, ml]

    This controls the addition of the -method parameter and its associated value. Set this property to the argument value required.

  property mlfrac

    cut-off freq for branch to appear in consensus (0.5-1.0)

    This controls the addition of the -mlfrac parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outgrno

    OTU to use as outgroup (starts from 0)

    This controls the addition of the -outgrno parameter and its associated value. Set this property to the argument value required.

  property outtreefile

    Phylip tree output file (optional)

    This controls the addition of the -outtreefile parameter and its associated value. Set this property to the argument value required.

  property root

    treat trees as rooted (YES, no)

    This controls the addition of the -root parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property trout

    treat trees as rooted (YES, no)

    This controls the addition of the -trout parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.WaterCommandline(cmd='water', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the water program from EMBOSS.

  __init__(cmd='water', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 637
  __static_attributes__ = ('parameters',)
  property aformat

    Display output in a different specified output format

    This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

  property asequence

    First sequence to align

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property brief

    Display brief identity and similarity

    This property controls the addition of the -brief switch, treat this property as a boolean.

  property bsequence

    Second sequence to align

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property datafile

    Matrix file

    This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gapextend

    Gap extension penalty

    This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap open penalty

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property nobrief

    Display extended identity and similarity

    This property controls the addition of the -nobrief switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property similarity

    Display percent identity and similarity

    This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

  property snucleotide

    Sequences are nucleotide (boolean)

    This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

  property sprotein

    Sequences are protein (boolean)

    This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.NeedleCommandline(cmd='needle', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the needle program from EMBOSS.

  __init__(cmd='needle', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 679
  __static_attributes__ = ('parameters',)
  property aformat

    Display output in a different specified output format

    This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

  property asequence

    First sequence to align

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property brief

    Display brief identity and similarity

    This property controls the addition of the -brief switch, treat this property as a boolean.

  property bsequence

    Second sequence to align

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property datafile

    Matrix file

    This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property endextend

    The score added to the end gap penalty for each base or residue in the end gap.

    This controls the addition of the -endextend parameter and its associated value. Set this property to the argument value required.

  property endopen

    The score taken away when an end gap is created.

    This controls the addition of the -endopen parameter and its associated value. Set this property to the argument value required.

  property endweight

    Apply And gap penalties

    This controls the addition of the -endweight parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gapextend

    Gap extension penalty

    This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap open penalty

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property nobrief

    Display extended identity and similarity

    This property controls the addition of the -nobrief switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property similarity

    Display percent identity and similarity

    This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

  property snucleotide

    Sequences are nucleotide (boolean)

    This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

  property sprotein

    Sequences are protein (boolean)

    This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.NeedleallCommandline(cmd='needleall', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the needleall program from EMBOSS.

  __init__(cmd='needleall', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 731
  __static_attributes__ = ('parameters',)
  property aformat

    Display output in a different specified output format

    This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

  property asequence

    First sequence to align

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property brief

    Display brief identity and similarity

    This property controls the addition of the -brief switch, treat this property as a boolean.

  property bsequence

    Second sequence to align

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property datafile

    Matrix file

    This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property endextend

    The score added to the end gap penalty for each base or residue in the end gap.

    This controls the addition of the -endextend parameter and its associated value. Set this property to the argument value required.

  property endopen

    The score taken away when an end gap is created.

    This controls the addition of the -endopen parameter and its associated value. Set this property to the argument value required.

  property endweight

    Apply And gap penalties

    This controls the addition of the -endweight parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property errorfile

    Error file to be written to.

    This controls the addition of the -errorfile parameter and its associated value. Set this property to the argument value required.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gapextend

    Gap extension penalty

    This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap open penalty

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property minscore

    Exclude alignments with scores below this threshold score.

    This controls the addition of the -minscore parameter and its associated value. Set this property to the argument value required.

  property nobrief

    Display extended identity and similarity

    This property controls the addition of the -nobrief switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property similarity

    Display percent identity and similarity

    This controls the addition of the -similarity parameter and its associated value. Set this property to the argument value required.

  property snucleotide

    Sequences are nucleotide (boolean)

    This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

  property sprotein

    Sequences are protein (boolean)

    This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.StretcherCommandline(cmd='stretcher', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the stretcher program from EMBOSS.

  __init__(cmd='stretcher', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 788
  __static_attributes__ = ('parameters',)
  property aformat

    Display output in a different specified output format

    This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

  property asequence

    First sequence to align

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property bsequence

    Second sequence to align

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property datafile

    Matrix file

    This controls the addition of the -datafile parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gapextend

    Gap extension penalty

    This controls the addition of the -gapextend parameter and its associated value. Set this property to the argument value required.

  property gapopen

    Gap open penalty

    This controls the addition of the -gapopen parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property snucleotide

    Sequences are nucleotide (boolean)

    This controls the addition of the -snucleotide parameter and its associated value. Set this property to the argument value required.

  property sprotein

    Sequences are protein (boolean)

    This controls the addition of the -sprotein parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FuzznucCommandline(cmd='fuzznuc', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fuzznuc program from EMBOSS.

  __init__(cmd='fuzznuc', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 831
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property complement

    Search complementary strand

    This controls the addition of the -complement parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property pattern

    Search pattern, using standard IUPAC one-letter codes

    This controls the addition of the -pattern parameter and its associated value. Set this property to the argument value required.

  property pmismatch

    Number of mismatches

    This controls the addition of the -pmismatch parameter and its associated value. Set this property to the argument value required.

  property rformat

    Specify the report format to output in.

    This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence database USA

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.FuzzproCommandline(cmd='fuzzpro', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the fuzzpro program from EMBOSS.

  __init__(cmd='fuzzpro', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 852
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property pattern

    Search pattern, using standard IUPAC one-letter codes

    This controls the addition of the -pattern parameter and its associated value. Set this property to the argument value required.

  property pmismatch

    Number of mismatches

    This controls the addition of the -pmismatch parameter and its associated value. Set this property to the argument value required.

  property rformat

    Specify the report format to output in.

    This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence database USA

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.Est2GenomeCommandline(cmd='est2genome', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the est2genome program from EMBOSS.

  __init__(cmd='est2genome', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 872
  __static_attributes__ = ('parameters',)
  property align

    Show the alignment.

    This controls the addition of the -align parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property best

    You can print out all comparisons instead of just the best

    This controls the addition of the -best parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property est

    EST sequence(s)

    This controls the addition of the -est parameter and its associated value. Set this property to the argument value required.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gappenalty

    Cost for deleting a single base in either sequence, excluding introns

    This controls the addition of the -gappenalty parameter and its associated value. Set this property to the argument value required.

  property genome

    Genomic sequence

    This controls the addition of the -genome parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property intronpenalty

    Cost for an intron, independent of length.

    This controls the addition of the -intronpenalty parameter and its associated value. Set this property to the argument value required.

  property match

    Score for matching two bases

    This controls the addition of the -match parameter and its associated value. Set this property to the argument value required.

  property minscore

    Exclude alignments with scores below this threshold score.

    This controls the addition of the -minscore parameter and its associated value. Set this property to the argument value required.

  property mismatch

    Cost for mismatching two bases

    This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

  property mode

    This determines the comparison mode. ‘both’, ‘forward’, or ‘reverse’

    This controls the addition of the -mode parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property reverse

    Reverse the orientation of the EST sequence

    This controls the addition of the -reverse parameter and its associated value. Set this property to the argument value required.

  property seed

    Random number seed

    This controls the addition of the -seed parameter and its associated value. Set this property to the argument value required.

  property shuffle

    Shuffle

    This controls the addition of the -shuffle parameter and its associated value. Set this property to the argument value required.

  property space

    for linear-space recursion.

    This controls the addition of the -space parameter and its associated value. Set this property to the argument value required.

  property splice

    Use donor and acceptor splice sites.

    This controls the addition of the -splice parameter and its associated value. Set this property to the argument value required.

  property splicepenalty

    Cost for an intron, independent of length and starting/ending on donor-acceptor sites

    This controls the addition of the -splicepenalty parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property width

    Alignment width

    This controls the addition of the -width parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.ETandemCommandline(cmd='etandem', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the etandem program from EMBOSS.

  __init__(cmd='etandem', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 921
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property maxrepeat

    Maximum repeat size

    This controls the addition of the -maxrepeat parameter and its associated value. Set this property to the argument value required.

  property minrepeat

    Minimum repeat size

    This controls the addition of the -minrepeat parameter and its associated value. Set this property to the argument value required.

  property mismatch

    Allow N as a mismatch

    This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property rformat

    Output report format

    This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property threshold

    Threshold score

    This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

  property uniform

    Allow uniform consensus

    This controls the addition of the -uniform parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.EInvertedCommandline(cmd='einverted', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the einverted program from EMBOSS.

  __init__(cmd='einverted', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 944
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gap

    Gap penalty

    This controls the addition of the -gap parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property match

    Match score

    This controls the addition of the -match parameter and its associated value. Set this property to the argument value required.

  property maxrepeat

    Maximum separation between the start and end of repeat

    This controls the addition of the -maxrepeat parameter and its associated value. Set this property to the argument value required.

  property mismatch

    Mismatch score

    This controls the addition of the -mismatch parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property threshold

    Minimum score threshold

    This controls the addition of the -threshold parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.PalindromeCommandline(cmd='palindrome', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the palindrome program from EMBOSS.

  __init__(cmd='palindrome', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 967
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property gaplimit

    Maximum gap between repeats

    This controls the addition of the -gaplimit parameter and its associated value. Set this property to the argument value required.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property maxpallen

    Maximum palindrome length

    This controls the addition of the -maxpallen parameter and its associated value. Set this property to the argument value required.

  property minpallen

    Minimum palindrome length

    This controls the addition of the -minpallen parameter and its associated value. Set this property to the argument value required.

  property nummismatches

    Number of mismatches allowed

    This controls the addition of the -nummismatches parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property overlap

    Report overlapping matches

    This controls the addition of the -overlap parameter and its associated value. Set this property to the argument value required.

  property sequence

    Sequence

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.TranalignCommandline(cmd='tranalign', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the tranalign program from EMBOSS.

  __init__(cmd='tranalign', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 1003
  __static_attributes__ = ('parameters',)
  property asequence

    Nucleotide sequences to be aligned.

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property bsequence

    Protein sequence alignment

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property outseq

    Output sequence file.

    This controls the addition of the -outseq parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property table

    Code to use

    This controls the addition of the -table parameter and its associated value. Set this property to the argument value required.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.DiffseqCommandline(cmd='diffseq', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the diffseq program from EMBOSS.

  __init__(cmd='diffseq', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 1032
  __static_attributes__ = ('parameters',)
  property aoutfeat

    File for output of first sequence’s features

    This controls the addition of the -aoutfeat parameter and its associated value. Set this property to the argument value required.

  property asequence

    First sequence to compare

    This controls the addition of the -asequence parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property boutfeat

    File for output of second sequence’s features

    This controls the addition of the -boutfeat parameter and its associated value. Set this property to the argument value required.

  property bsequence

    Second sequence to compare

    This controls the addition of the -bsequence parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property rformat

    Output report file format

    This controls the addition of the -rformat parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property wordsize

    Word size to use for comparisons (10 default)

    This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.

class Bio.Emboss.Applications.IepCommandline(cmd='iep', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline for EMBOSS iep: calculated isoelectric point and charge.

  Examples

      >>> from Bio.Emboss.Applications import IepCommandline
      >>> iep_cline = IepCommandline(sequence="proteins.faa",
      ...                            outfile="proteins.txt")
      >>> print(iep_cline)
      iep -outfile=proteins.txt -sequence=proteins.faa

  You would typically run the command line with iep_cline() or via the Python subprocess module, as described in the Biopython tutorial.

  __init__(cmd='iep', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 1072
  __static_attributes__ = ('parameters',)
  property amino

    Number of N-termini

    > Integer 0 (default) or more.

    This controls the addition of the -amino parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property carboxyl

    Number of C-termini

    > Integer 0 (default) or more.

    This controls the addition of the -carboxyl parameter and its associated value. Set this property to the argument value required.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property disulphides

    Number of disulphide bridges

    > Integer 0 (default) or more.

    This controls the addition of the -disulphides parameter and its associated value. Set this property to the argument value required.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property lysinemodified

    Number of modified lysines

    > Integer 0 (default) or more.

    This controls the addition of the -lysinemodified parameter and its associated value. Set this property to the argument value required.

  property notermini

    Exclude (True) or include (False) charge at N and C terminus.

    This controls the addition of the -notermini parameter and its associated value. Set this property to the argument value required.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property sequence

    Protein sequence(s) filename

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.SeqretCommandline(cmd='seqret', **kwargs)

  Bases: `_EmbossMinimalCommandLine`

  Commandline object for the seqret program from EMBOSS.

  This tool allows you to interconvert between different sequence file formats (e.g. GenBank to FASTA). Combining Biopython’s Bio.SeqIO module with seqret using a suitable intermediate file format can allow you to read/write to an even wider range of file formats.

  This wrapper currently only supports the core functionality, things like feature tables (in EMBOSS 6.1.0 onwards) are not yet included.

  __init__(cmd='seqret', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 1135
  __static_attributes__ = ('parameters',)
  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property osformat

    Output sequence(s) format (e.g. fasta, genbank)

    This controls the addition of the -osformat parameter and its associated value. Set this property to the argument value required.

  property outseq

    Output sequence file.

    This controls the addition of the -outseq parameter and its associated value. Set this property to the argument value required.

  property sequence

    Input sequence(s) filename

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property sformat

    Input sequence(s) format (e.g. fasta, genbank)

    This controls the addition of the -sformat parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

class Bio.Emboss.Applications.SeqmatchallCommandline(cmd='seqmatchall', **kwargs)

  Bases: `_EmbossCommandLine`

  Commandline object for the seqmatchall program from EMBOSS.

  e.g. >>> cline = SeqmatchallCommandline(sequence=”opuntia.fasta”, outfile=”opuntia.txt”) >>> cline.auto = True >>> cline.wordsize = 18 >>> cline.aformat = “pair” >>> print(cline) seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair

  __init__(cmd='seqmatchall', **kwargs)

    Initialize the class.

  __annotations__ = {}
  __firstlineno__ = 1182
  __static_attributes__ = ('parameters',)
  property aformat

    Display output in a different specified output format

    This controls the addition of the -aformat parameter and its associated value. Set this property to the argument value required.

  property auto

    Turn off prompts.

    Automatic mode disables prompting, so we recommend you set this argument all the time when calling an EMBOSS tool from Biopython.

    This property controls the addition of the -auto switch, treat this property as a boolean.

  property debug

    Write debug output to program.dbg.

    This property controls the addition of the -debug switch, treat this property as a boolean.

  property die

    Report dying program messages.

    This property controls the addition of the -die switch, treat this property as a boolean.

  property error

    Report errors.

    This property controls the addition of the -error switch, treat this property as a boolean.

  property filter

    Read standard input, write standard output.

    This property controls the addition of the -filter switch, treat this property as a boolean.

  property help

    Report command line options.

    More information on associated and general qualifiers can be found with -help -verbose

    This property controls the addition of the -help switch, treat this property as a boolean.

  property options

    Prompt for standard and additional values.

    If you are calling an EMBOSS tool from within Biopython, we DO NOT recommend using this option.

    This property controls the addition of the -options switch, treat this property as a boolean.

  property outfile

    Output filename

    This controls the addition of the -outfile parameter and its associated value. Set this property to the argument value required.

  property sequence

    Readable set of sequences

    This controls the addition of the -sequence parameter and its associated value. Set this property to the argument value required.

  property stdout

    Write standard output.

    This property controls the addition of the -stdout switch, treat this property as a boolean.

  property verbose

    Report some/full command line options

    This property controls the addition of the -verbose switch, treat this property as a boolean.

  property warning

    Report warnings.

    This property controls the addition of the -warning switch, treat this property as a boolean.

  property wordsize

    Word size (Integer 2 or more, default 4)

    This controls the addition of the -wordsize parameter and its associated value. Set this property to the argument value required.

Biopython v: 1.85

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